Information & Computational Sciences

Barley epigenome

Barley epigenome browser

The barley epigenome browser is a JBrowse based genome browser for visualising barley histone modification data. The research is described in Baker et al (2015) Chromatin state analysis of the barley epigenome reveals a higher order structure defined by H3K27me1 and H3K27me3 abundance Plant J. 84:111-124. Chromosome sequences were manually assembled by incorporating PopSeq and IBGSC genetic map data to order as many Morex V3 contigs as possible. Gene and TE annotations from the IBGSC were then related to the new pseudo genome locations and are also available as tracks in the epigenome browser. To search for a gene of interest in the browser use the search bar next to the chromosome drop-down menu. Chromatin states were defined with ChromHMM and mapped to the genome. Coordinate files detailing the position of contigs, genes and TEs can be downloaded as gzipped files in the links at the bottom of this page. Histone modification peaks were called against the pseudo genome, but locations have been related back to individual contigs and are available to download below.

As part of my personal development (and love of audio), I started listening to a lot of tech podcasts this year. Over the years I have occasionally listened to Michael Kennedy’s ‘Talk Python to me’, it is only more recently I have really started to explore this form of learning. The purpose of this blog […]